RetrogeneDB ID: retro_mmus_202

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:72304908..72305181(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000070713
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Hmgn2
• Ensembl ID: ENSMUSG00000003038
• Aliases: Hmgn2, HMG-17, Hmg17
• Description: high mobility group nucleosomal binding domain 2 [Source:MGI Symbol;Acc:MGI:96136]

Sequence

>retro_mmus_202
ATGCCCAAAAGAAAGGCTGAAGGGGATGCTAAAGGAGACAAAACCAAGGTGAAGGACGAGCCACAGAGAAGATCTGCGAG
GTTGTCTGCTAAACCTGCTCCTCCAAAGCCAGAGCCCAAACCTAAAAAGGCCCCTGCGAAGAAGGGAGAGAAGGTACCCA
AGGGGAAGAAGGGGAAAGCTGACGCCGGGAAGGATGCGAATAATCCTGCAGAAAATGGAGATGCCAAAACAGACCAGGCA
CAGAAAGCTGAAGGTGCTGGAGATGCCAAGTGA

Alignment

ORF - retro_mmus_202 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPKRKAEGDAKGDKTKVKDEPQRRSARLSAKPAPPKPEPKPKKAPAKKGEKVPKGKKGKADAGKDANNPA
          MPKRKAEGDAKGDKTKVKDEPQRRSARLSAKPAPPKPEPKPKKAPAKKGEKVPKGKKGKADAGKDANNPA
Retrocopy MPKRKAEGDAKGDKTKVKDEPQRRSARLSAKPAPPKPEPKPKKAPAKKGEKVPKGKKGKADAGKDANNPA

Parental  ENGDAKTDQAQKAEGAGDAK
          ENGDAKTDQAQKAEGAGDAK
Retrocopy ENGDAKTDQAQKAEGAGDAK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.00 RPM	19.77 RPM
SRP007412_cerebellum	0.00 RPM	13.72 RPM
SRP007412_heart	0.00 RPM	21.67 RPM
SRP007412_kidney	0.00 RPM	16.23 RPM
SRP007412_liver	0.00 RPM	7.67 RPM
SRP007412_testis	0.00 RPM	11.39 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_202 was not detected

EST

No EST(s) were mapped for retro_mmus_202 retrocopy.

TSS

No TSS is located nearby retro_mmus_202 retrocopy 5' end.

Lab

retro_mmus_202 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_202 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 390 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000038104	7 retrocopies	retro_btau_1041, retro_btau_1160, retro_btau_1200, retro_btau_1292, retro_btau_1297, retro_btau_1684, retro_btau_482,
Canis familiaris	ENSCAFG00000023168	35 retrocopies	retro_cfam_1043, retro_cfam_1188, retro_cfam_1314, retro_cfam_1360, retro_cfam_1519, retro_cfam_1546, retro_cfam_1593, retro_cfam_1606, retro_cfam_1629, retro_cfam_1681, retro_cfam_1708, retro_cfam_1784, retro_cfam_1989, retro_cfam_2060, retro_cfam_2097, retro_cfam_2133, retro_cfam_266, retro_cfam_317, retro_cfam_324, retro_cfam_351, retro_cfam_353, retro_cfam_38, retro_cfam_381, retro_cfam_410, retro_cfam_446, retro_cfam_538, retro_cfam_623, retro_cfam_628, retro_cfam_705, retro_cfam_745, retro_cfam_783, retro_cfam_795, retro_cfam_821, retro_cfam_845, retro_cfam_860,
Dasypus novemcinctus	ENSDNOG00000018469	56 retrocopies	retro_dnov_1067, retro_dnov_1087, retro_dnov_112, retro_dnov_1178, retro_dnov_1316, retro_dnov_1321, retro_dnov_1350, retro_dnov_1409, retro_dnov_1414, retro_dnov_1461, retro_dnov_1518, retro_dnov_155, retro_dnov_1551, retro_dnov_1552, retro_dnov_1563, retro_dnov_1962, retro_dnov_1992, retro_dnov_2011, retro_dnov_2017, retro_dnov_2099, retro_dnov_2105, retro_dnov_2111, retro_dnov_2131, retro_dnov_2227, retro_dnov_2254, retro_dnov_2274, retro_dnov_2314, retro_dnov_2333, retro_dnov_2366, retro_dnov_2384, retro_dnov_2415, retro_dnov_2441, retro_dnov_2510, retro_dnov_2541, retro_dnov_2550, retro_dnov_2596, retro_dnov_2630, retro_dnov_2688, retro_dnov_354, retro_dnov_37, retro_dnov_411, retro_dnov_419, retro_dnov_478, retro_dnov_48, retro_dnov_495, retro_dnov_541, retro_dnov_583, retro_dnov_587, retro_dnov_717, retro_dnov_732, retro_dnov_79, retro_dnov_808, retro_dnov_809, retro_dnov_912, retro_dnov_916, retro_dnov_995,
Dipodomys ordii	ENSDORG00000001787	3 retrocopies	retro_dord_10, retro_dord_401, retro_dord_511,
Echinops telfairi	ENSETEG00000013571	33 retrocopies	retro_etel_1035, retro_etel_1097, retro_etel_1210, retro_etel_1253, retro_etel_1282, retro_etel_1298, retro_etel_1314, retro_etel_1346, retro_etel_1398, retro_etel_1582, retro_etel_165, retro_etel_1690, retro_etel_1710, retro_etel_178, retro_etel_1836, retro_etel_1845, retro_etel_1939, retro_etel_1945, retro_etel_1951, retro_etel_1961, retro_etel_2079, retro_etel_253, retro_etel_292, retro_etel_298, retro_etel_446, retro_etel_481, retro_etel_505, retro_etel_511, retro_etel_571, retro_etel_61, retro_etel_768, retro_etel_819, retro_etel_881,
Felis catus	ENSFCAG00000012812	3 retrocopies	retro_fcat_1842, retro_fcat_4, retro_fcat_530,
Homo sapiens	ENSG00000198830	51 retrocopies	retro_hsap_100, retro_hsap_114, retro_hsap_1208, retro_hsap_1368, retro_hsap_1395, retro_hsap_1427, retro_hsap_1471, retro_hsap_1492, retro_hsap_1512, retro_hsap_1517, retro_hsap_1518, retro_hsap_1586, retro_hsap_1670, retro_hsap_1684, retro_hsap_1787, retro_hsap_1834, retro_hsap_1931, retro_hsap_1934, retro_hsap_2082, retro_hsap_2116, retro_hsap_2296, retro_hsap_2309, retro_hsap_233, retro_hsap_2564, retro_hsap_2592, retro_hsap_2728, retro_hsap_273, retro_hsap_2755, retro_hsap_2779, retro_hsap_2849, retro_hsap_2914, retro_hsap_318, retro_hsap_3189, retro_hsap_3339, retro_hsap_3372, retro_hsap_3412, retro_hsap_3515, retro_hsap_3616, retro_hsap_3755, retro_hsap_3896, retro_hsap_4124, retro_hsap_4138, retro_hsap_4297, retro_hsap_4791, retro_hsap_4914, retro_hsap_601, retro_hsap_688, retro_hsap_689, retro_hsap_718, retro_hsap_793, retro_hsap_849,
Gorilla gorilla	ENSGGOG00000000971	11 retrocopies	retro_ggor_114, retro_ggor_146, retro_ggor_162, retro_ggor_166, retro_ggor_182, retro_ggor_186, retro_ggor_197, retro_ggor_23, retro_ggor_38, retro_ggor_40, retro_ggor_54,
Macropus eugenii	ENSMEUG00000010966	8 retrocopies	retro_meug_1178, retro_meug_126, retro_meug_1859, retro_meug_1910, retro_meug_1997, retro_meug_248, retro_meug_369, retro_meug_76,
Mus musculus	ENSMUSG00000003038	2 retrocopies	retro_mmus_202 , retro_mmus_2582,
Otolemur garnettii	ENSOGAG00000032571	14 retrocopies	retro_ogar_1438, retro_ogar_1445, retro_ogar_1603, retro_ogar_1668, retro_ogar_1687, retro_ogar_1998, retro_ogar_2097, retro_ogar_2210, retro_ogar_2231, retro_ogar_2424, retro_ogar_287, retro_ogar_2989, retro_ogar_3411, retro_ogar_52,
Ochotona princeps	ENSOPRG00000001616	5 retrocopies	retro_opri_1202, retro_opri_161, retro_opri_532, retro_opri_730, retro_opri_853,
Pongo abelii	ENSPPYG00000001682	16 retrocopies	retro_pabe_1182, retro_pabe_1511, retro_pabe_1977, retro_pabe_1989, retro_pabe_206, retro_pabe_2263, retro_pabe_23, retro_pabe_2601, retro_pabe_3, retro_pabe_3480, retro_pabe_366, retro_pabe_396, retro_pabe_533, retro_pabe_535, retro_pabe_589, retro_pabe_696,
Pan troglodytes	ENSPTRG00000000386	54 retrocopies	retro_ptro_1011, retro_ptro_1024, retro_ptro_1026, retro_ptro_1027, retro_ptro_1040, retro_ptro_1053, retro_ptro_1067, retro_ptro_1094, retro_ptro_1197, retro_ptro_1235, retro_ptro_128, retro_ptro_1291, retro_ptro_1292, retro_ptro_1495, retro_ptro_1516, retro_ptro_1532, retro_ptro_1549, retro_ptro_1625, retro_ptro_1633, retro_ptro_1837, retro_ptro_1844, retro_ptro_1863, retro_ptro_1880, retro_ptro_1929, retro_ptro_1970, retro_ptro_203, retro_ptro_2255, retro_ptro_229, retro_ptro_2292, retro_ptro_2317, retro_ptro_2387, retro_ptro_2445, retro_ptro_2461, retro_ptro_2549, retro_ptro_257, retro_ptro_2650, retro_ptro_2801, retro_ptro_2812, retro_ptro_2840, retro_ptro_2913, retro_ptro_2970, retro_ptro_3187, retro_ptro_3276, retro_ptro_445, retro_ptro_493, retro_ptro_495, retro_ptro_512, retro_ptro_543, retro_ptro_552, retro_ptro_59, retro_ptro_590, retro_ptro_827, retro_ptro_939, retro_ptro_958,
Pteropus vampyrus	ENSPVAG00000017269	5 retrocopies	retro_pvam_1046, retro_pvam_1059, retro_pvam_1065, retro_pvam_379, retro_pvam_4,
Sorex araneus	ENSSARG00000013139	3 retrocopies	retro_sara_12, retro_sara_17, retro_sara_176,
Sus scrofa	ENSSSCG00000003555	3 retrocopies	retro_sscr_573, retro_sscr_66, retro_sscr_985,
Tupaia belangeri	ENSTBEG00000016632	33 retrocopies	retro_tbel_1351, retro_tbel_16, retro_tbel_1844, retro_tbel_21, retro_tbel_2219, retro_tbel_2498, retro_tbel_2670, retro_tbel_3050, retro_tbel_309, retro_tbel_3101, retro_tbel_3112, retro_tbel_3121, retro_tbel_3149, retro_tbel_320, retro_tbel_3413, retro_tbel_3462, retro_tbel_36, retro_tbel_389, retro_tbel_4058, retro_tbel_417, retro_tbel_4469, retro_tbel_448, retro_tbel_4615, retro_tbel_4644, retro_tbel_475, retro_tbel_50, retro_tbel_538, retro_tbel_62, retro_tbel_65, retro_tbel_66, retro_tbel_704, retro_tbel_732, retro_tbel_757,
Tarsius syrichta	ENSTSYG00000011519	42 retrocopies	retro_tsyr_114, retro_tsyr_1156, retro_tsyr_1165, retro_tsyr_1199, retro_tsyr_1227, retro_tsyr_1255, retro_tsyr_1270, retro_tsyr_13, retro_tsyr_1357, retro_tsyr_138, retro_tsyr_1382, retro_tsyr_1394, retro_tsyr_143, retro_tsyr_1487, retro_tsyr_1488, retro_tsyr_1506, retro_tsyr_1510, retro_tsyr_1551, retro_tsyr_1618, retro_tsyr_163, retro_tsyr_168, retro_tsyr_1680, retro_tsyr_1878, retro_tsyr_1881, retro_tsyr_1970, retro_tsyr_2019, retro_tsyr_2134, retro_tsyr_256, retro_tsyr_280, retro_tsyr_325, retro_tsyr_333, retro_tsyr_594, retro_tsyr_611, retro_tsyr_668, retro_tsyr_675, retro_tsyr_726, retro_tsyr_772, retro_tsyr_83, retro_tsyr_857, retro_tsyr_927, retro_tsyr_959, retro_tsyr_97,
Tursiops truncatus	ENSTTRG00000005681	5 retrocopies	retro_ttru_1392, retro_ttru_1443, retro_ttru_3, retro_ttru_345, retro_ttru_788,
Vicugna pacos	ENSVPAG00000008076	1 retrocopy	retro_vpac_183,